Last updated: 2018-08-27
workflowr checks: (Click a bullet for more information) ✔ R Markdown file: up-to-date
Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.
✔ Environment: empty
Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.
✔ Seed:
set.seed(20180723)
The command set.seed(20180723) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.
✔ Session information: recorded
Great job! Recording the operating system, R version, and package versions is critical for reproducibility.
✔ Repository version: 5f154f3
wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
Ignored files:
Ignored: .DS_Store
Ignored: .Rhistory
Ignored: .Rproj.user/
Ignored: analysis/.DS_Store
Ignored: analysis/.Rhistory
Ignored: docs/.DS_Store
Ignored: docs/figure/.DS_Store
Untracked files:
Untracked: analysis/fifthheatmap.pdf
Untracked: analysis/firstheatmap.pdf
Untracked: analysis/fourthheatmap.pdf
Untracked: analysis/heatmap.pdf
Untracked: analysis/secondheatmap.pdf
Untracked: analysis/test.tsv
Untracked: analysis/thirdheatmap.pdf
Untracked: docs/figure/correlation analysis.Rmd/
Untracked: docs/figure/drug.Rmd/
Untracked: docs/figure/gene_set_analysis_re.Rmd/
Untracked: docs/fourthheatmap.pdf
Unstaged changes:
Modified: analysis/_site.yml
Modified: analysis/drugresponse.Rmd
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 5f154f3 | bingrus | 2018-08-27 | wflow_publish(“analysis/correlation_analysis.Rmd”) |
| html | b8e04c6 | bingrus | 2018-08-20 | Build site. |
| html | e18ffda | bingrus | 2018-08-20 | Build site. |
| Rmd | ca2b21d | bingrus | 2018-08-20 | wflow_git_commit(“analysis/correlation_analysis.Rmd”) |
| html | 763aeb4 | bingrus | 2018-08-20 | Build site. |
| Rmd | 10c7b44 | bingrus | 2018-08-20 | wflow_publish(“analysis/correlation_analysis.Rmd”) |
| html | 64138e4 | bingrus | 2018-08-20 | Build site. |
| Rmd | f418829 | bingrus | 2018-08-20 | wflow_publish(“analysis/correlation_analysis.Rmd”) |
| html | 3e44254 | bingrus | 2018-08-20 | Build site. |
| Rmd | 2b7366e | bingrus | 2018-08-20 | wflow_git_commit(“analysis/correlation_analysis.Rmd”) |
| Version | Author | Date |
|---|---|---|
| 3d385b8 | bingrus | 2018-08-20 |
| Version | Author | Date |
|---|---|---|
| 3d385b8 | bingrus | 2018-08-20 |
sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.4
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] grid parallel stats4 stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] bindrcpp_0.2.2 knitr_1.20 heatmaply_0.15.2
[4] viridis_0.5.1 viridisLite_0.3.0 plotly_4.8.0
[7] gplots_3.0.1 GO.db_3.6.0 GSEABase_1.42.0
[10] graph_1.58.0 GSVA_1.28.0 reshape_0.8.7
[13] ggplot2_3.0.0 GEOquery_2.48.0 annotate_1.58.0
[16] XML_3.98-1.11 org.Hs.eg.db_3.6.0 AnnotationDbi_1.42.1
[19] IRanges_2.14.10 S4Vectors_0.18.3 Biobase_2.40.0
[22] BiocGenerics_0.26.0 limma_3.36.2 htmlwidgets_1.2
loaded via a namespace (and not attached):
[1] colorspace_1.3-2 class_7.3-14 modeltools_0.2-22
[4] mclust_5.4.1 rprojroot_1.3-2 flexmix_2.3-14
[7] bit64_0.9-7 mvtnorm_1.0-8 xml2_1.2.0
[10] codetools_0.2-15 R.methodsS3_1.7.1 robustbase_0.93-2
[13] geneplotter_1.58.0 shinythemes_1.1.1 jsonlite_1.5
[16] workflowr_1.1.1 cluster_2.0.7-1 kernlab_0.9-26
[19] R.oo_1.22.0 shiny_1.1.0 readr_1.1.1
[22] compiler_3.5.0 httr_1.3.1 backports_1.1.2
[25] assertthat_0.2.0 lazyeval_0.2.1 later_0.7.3
[28] htmltools_0.3.6 tools_3.5.0 gtable_0.2.0
[31] glue_1.2.0 dplyr_0.7.6 Rcpp_0.12.17
[34] trimcluster_0.1-2.1 gdata_2.18.0 crosstalk_1.0.0
[37] iterators_1.0.10 fpc_2.1-11.1 stringr_1.3.1
[40] mime_0.5 gtools_3.8.1 dendextend_1.8.0
[43] DEoptimR_1.0-8 MASS_7.3-50 scales_0.5.0
[46] TSP_1.1-6 hms_0.4.2 promises_1.0.1
[49] RColorBrewer_1.1-2 yaml_2.1.19 memoise_1.1.0
[52] gridExtra_2.3 stringi_1.2.3 RSQLite_2.1.1
[55] gclus_1.3.1 foreach_1.4.4 seriation_1.2-3
[58] caTools_1.17.1 rlang_0.2.1 pkgconfig_2.0.1
[61] prabclus_2.2-6 bitops_1.0-6 evaluate_0.10.1
[64] lattice_0.20-35 purrr_0.2.5 bindr_0.1.1
[67] bit_1.1-14 tidyselect_0.2.4 plyr_1.8.4
[70] magrittr_1.5 R6_2.2.2 DBI_1.0.0
[73] pillar_1.2.3 whisker_0.3-2 withr_2.1.2
[76] RCurl_1.95-4.10 nnet_7.3-12 tibble_1.4.2
[79] KernSmooth_2.23-15 rmarkdown_1.10 data.table_1.11.4
[82] blob_1.1.1 git2r_0.22.1 digest_0.6.15
[85] diptest_0.75-7 webshot_0.5.0 xtable_1.8-2
[88] tidyr_0.8.1 httpuv_1.4.4.2 R.utils_2.6.0
[91] munsell_0.5.0 registry_0.5
This reproducible R Markdown analysis was created with workflowr 1.1.1